Mentype Nonaplex I PCR Amplification Kit

Transcription

1 Mentype Nonaplex I PCR Amplification Kit Instructions for use The Mentype Nonaplex I PCR Amplification Kit is a multiplex application for the Short Tandem Repeat (STR) loci, which belong to the German Forensic DNA Database and are recommended by EDNAP. In one PCR reaction, the eight polymorphic STR loci D3S1358, D8S1179, D18S51, D21S11, FGA (FIBRA), SE33 (ACTBP2), TH01 (TC11), and vwa as well as the gender-specific Amelogenin are amplified simultaneously. 100, 400, Mai Biotype Diagnostic GmbH Moritzburger Weg 67 D Dresden Germany Made in Germany

2 2 Biotype Diagnostic GmbH develops, produces and distributes PCR-based applications for medical diagnostics. For more information and enquiries please contact us: Tel.: (Mo to Fr, 9 am to 5 pm) support@biotype.de Our Mentype test kits guarantee the highest quality standards for clinics and research. Mentype Nonaplex I NONAIGA01v1en

3 3 Trademarks and patents Mentype is a registered trademark of Biotype Diagnostic GmbH. ABI PRISM, GeneScan, Genotyper, GeneMapper and Applied Biosystems are registered trademarks of Applied Biosystems Inc. or its subsidiaries in the U.S. and certain other countries. 6-FAM, HEX, NED, ROX, POP-4 and Hi-Di are trademarks of Applied Biosystems Inc. GeneAmp is a registered trademark of Roche Molecular Systems. The PCR is covered by patents. Patentees are Hoffmann-La Roche Inc. and F. Hoffmann-La Roche (Roche). GenBank is a trademark of National Institute of Health. NOTICE TO PURCHASER: LIMITED LICENSE This product is sold under licensing arrangements between Licensee and Life Technologies Corporation. The purchase price of this product includes limited, nontransferable rights under certain U.S. and foreign patent(s) owned by Life Technologies Corporation to use only this amount of the product to practice the claims in said patents solely for activities of the purchaser in the field of human or animal identification. No other rights are conveyed. Further information on purchasing licenses under the above patents may be obtained by contacting the Licensing Department, Life Technologies Corporation, 5791 Van Allen Way, Carlsbad, California outlicensing@lifetech.com. Warnings and safety instructions The PCR Amplification Kit contains the following potentially hazardous chemicals: Kit component Chemical Hazards Primer mix, reaction mix Sodium azide NaN 3 toxic if swallowed, develops toxic gases and allelic ladder when it gets in contact with acids Observe the Material Safety Data Sheets (MSDS) for all Biotype products, which are available on request. Please contact the respective manufacturers for copies of the MSDS for any additionally needed reagents. Biotype Diagnostic GmbH, all rights reserved Mentype Nonaplex I NONAIGA01v1en

4 4 Content 1. Product description Protocols for amplification and electrophoresis PCR amplification Electrophoresis using the ABI PRISM 310 Genetic Analyzer Electrophoresis using the ABI PRISM 3130/3130xl Genetic Analyzer Analysis parameter / analysis method Biotype template files Controls Lengths of fragments and alleles Interpretation of results References Mentype Nonaplex I NONAIGA01v1en

5 5 1. Product description The Mentype Nonaplex I PCR Amplification Kit is a multiplex application for the Short Tandem Repeat (STR) loci, which belong to the German Forensic DNA Database and are recommended by EDNAP. In one PCR reaction, the eight polymorphic STR loci D3S1358, D8S1179, D18S51, D21S11, FGA (FIBRA), SE33 (ACTBP2), TH01 (TC11), and vwa as well as the gender-specific Amelogenin are amplified simultaneously. This application was developed for fast and reliable DNA genotyping of blood, buccal swabs and forensic stains. The primers are fluorescence-labelled with 6-FAM (Amelogenin, D3S1358, TH01, and SE33), HEX (vwa, FGA, and D18S51) or NED (D8S1179 and D21S11). For genotyping of rare FGA alleles ( ), we recommend to use Mentype Nonaplex QS. The detection limit of Mentype Nonaplex I PCR Amplification Kit is less than 200 pg genomic DNA. However, it is recommended to use ng DNA. The test kit was validated and evaluated using the GeneAmp 9700 thermal cycler, ABI PRISM 310 Genetic Analyzer, and ABI PRISM 3100/3130 Genetic Analyzer. Table 1. Locus-specific information of Mentype Nonaplex I Locus GenBank accession Repeat motif of the reference allele Reference allele Allele range Amelogenin X M55418 Amelogenin Y M55419 D3S TCTA [TCTG] 2 [TCTA] D8S1179 G08710 [TCTA] D18S51 L18333 [AGAA] D21S11 AP [TCTA] 4 [TCTG] 6 [TCTA] 3 TA [TCTA] TCA [TCTA] 2 TCCATA [TCTA] 11 FGA (FIBRA) M64982 [TTTC] 3 TTTTTTCT [CTTT] 13 CTCC [TTCC] 2 SE33 (ACTBP2) NG [AAAG] 9 AA [AAAG] TH01 (TC11) D00269 [TCAT] vwa M25858 TCTA [TCTG] 4 [TCTA] Table 1 shows the STR loci with their repeat motifs and alleles that are concordant with the International Society for Forensic Genetics (ISFG) guidelines for the use of microsatellite markers (Bär et al., 1997). Allele ranges include all known alleles of the National Institute of Standards and Technology (NIST as at 12/2008) and of the current literature. Mentype Nonaplex I NONAIGA01v1en

6 6 Table 2. Chromosomal mapping of Mentype Nonaplex I Locus Chromosomal mapping Amelogenin X Xp Amelogenin Y Yp11.2 D3S1358 3p25.3 D8S1179 8q D18S51 18q21.3 D21S11 21q21.1 FGA (FIBRA) 4q28.2 SE33 6q14.2 TH01 11p15.5pter vwa 12p13.31 Content Mentype Nonaplex I PCR Amplification Kit (100 Reactions) Nuclease-free water 3.0 ml Reaction mix A 500 µl Primer mix 250 µl DNA polymerase 40 µl Control DNA XY1 (2 ng/µl) 10 µl DNA Size Standard 550 (ROX) 50 µl Allelic ladder 10 µl Storage Store all components at 20 C and avoid repeated thawing and freezing. Primer mix and allelic ladder must be stored protected from light. The DNA samples and post-pcr reagents (allelic ladder and DNA size standard) should be stored separately from the PCR reagents. The expiry date is indicated on the kit cover. Quality assurance All kit components undergo an intensive quality assurance process at Biotype Diagnostic GmbH. The quality of the test kits is permanently monitored in order to ensure unrestricted usability. Please contact us if you have any questions regarding quality assurance. Mentype Nonaplex I NONAIGA01v1en

7 7 Additional required reagents Additional reagents are needed in order to use the Biotype PCR Amplification Kit: Reagent Supplier Order number Hi-Di Formamide, 25 ml Applied Biosystems Matrix Standards DS-30 for ABI PRISM 310 Genetic Analyzer Applied Biosystems and (NED) Matrix Standards DS-30 for ABI PRISM multi-capillary instruments Applied Biosystems Mentype Nonaplex I NONAIGA01v1en

8 8 2. Protocols for amplification and electrophoresis 2.1 PCR amplification Master mix preparation The table below shows the volumes of all PCR reagents per 25 µl reaction volume, including a sample volume of 1.0 µl (template DNA). The number of reactions to be set up shall be determined taking into account positive and negative control reactions. Add one or two reactions to this number to compensate the pipetting error. Component Volume Nuklease-free water 16.1 µl Reaction mix A* 5.0 µl Primer mix 2.5 µl Multi Taq2 DNA Polymerase (hot start, 2.5 U/µL) 0.4 µl Volume of master mix 24.0 µl * contains Mg 2+, dntps, BSA All components should be mixed (vortex) and centrifuged for about 10 s before preparing the master mix. The DNA volume applied to the assay depends on its concentration. A volume of up to 5 µl may be necessary for DNA trace templates. DNA volumes of more than 5 µl are not recommended, because potential PCR inhibitors may interfere with the process. Fill up the final reaction volume to 25 µl with nuclease-free water. Generally, DNA templates shall be stored in nuclease-free water or in diluted TE buffer (10 mm Tris HCl, ph 8.0 and 1 mm EDTA), e.g. 0.1x TE buffer. The primer mixes are adjusted for balanced peak heights at 30 PCR cycles and 0.5 ng Control DNA XY1 in a reaction volume of 25 µl. If more DNA template is introduced, higher peaks can be expected for small PCR fragments and relatively low peaks for large fragments. Reduce the amount of DNA template to correct this imbalance. Positive control For the positive amplification control, dilute the Control DNA XY1 to 0.5 ng in the appropriate volume. Instead of the template DNA pipette the diluted Control DNA into a reaction tube containing the PCR master mix. Negative control For the negative amplification control, pipette nuclease-free water instead of template DNA into a reaction tube containing the PCR master mix. Mentype Nonaplex I NONAIGA01v1en

9 9 PCR amplification parameter Perform a hot start PCR in order to activate the Multi Taq2 DNA Polymerase and to prevent the formation of non-specific amplification products. The number of cycles depends on the amount of DNA. 30 cycles are recommended for all samples. For critical stains (< 100 pg DNA), it is recommended to increase the number of PCR cycles from 30 to 34. Standard method Recommended for all DNA samples Temperature Time 94 C 4 min (hot start for activation of the Multi Taq2 DNA Polymerase) 94 C 30 s 58 C 120 s 30 cycles 72 C 75 s 68 C 60 min 10 C hold Optional Recommended for stains with small amounts of DNA Temperature Time 94 C 4 min (hot start for activation of the Multi Taq2 DNA Polymerase) 94 C 30 s 58 C 120 s 34 cycles 72 C 75 s 68 C 60 min 10 C hold Too small amounts of DNA may result in allelic dropouts and imbalances of the peaks. Furthermore, unspecific amplification products could appear. With increasing numbers of cycles, there is the risk of cross contamination caused by minimal amounts of impurities. Mentype Nonaplex I NONAIGA01v1en

10 Electrophoresis using the ABI PRISM 310 Genetic Analyzer For general instructions on instrument setup, matrix generation and application of the GeneScan or GeneMapper ID software, refer to the ABI PRISM 310 Genetic Analyzer User s Manual. Electrophoresis using the GeneScan software is described below. The virtual filter set D shall be used for combined application of the four fluorescent labels 6-FAM, HEX, NED, and ROX (also called DS-30). Generally, Filter Sets A and F are suitable, too. Material Capillary Polymer Buffer 47 cm / 50 µm (green) POP-4 for 310 Genetic Analyzer 10x Genetic Analyzer Buffer with EDTA Matrix generation Prior to conducting DNA fragment size analysis with the filter set D, a matrix with the four fluorescent labels 6-FAM, HEX, NED, and ROX must be generated. The suitable matrix standard DS-30 is available from Applied Biosystems. Colour Matrix standard Order number Blue (B) 6-FAM Applied Biosystems, Green (G) HEX Applied Biosystems, Yellow (Y) NED Applied Biosystems, Red (R) ROX Applied Biosystems, Four electrophoresis runs shall be conducted, one for each fluorescent label, 6-FAM, HEX, NED, and ROX, under the same conditions as for the samples and allelic ladders of the Biotype test kit to generate suitable matrix files. Matrix sample Component Volume Hi-Di Formamide 12.0 µl Matrix sample 1 Matrix standard 6-FAM 1.0 µl Matrix sample 2 Matrix sample 3 Hi-Di Formamide 12.0 µl Matrix standard HEX 1.0 µl Hi-Di Formamide 12.0 µl Matrix standard NED 1.0 µl Hi-Di Formamide 12.0 µl Matrix sample 4 Matrix standard ROX 1.0 µl - Denaturation for 3 min at 95 C - Cool down to 4 C - For analysis: load the samples on the tray - Create a Sample Sheet and enter sample designation Mentype Nonaplex I NONAIGA01v1en

11 11 Injection list for matrix generation Parameter Set up Module File GS STR POP-4 (1 ml) D Matrix File NONE Size Standard* NONE Injection [s] 5 Injection [kv] 15.0 Run [kv] 15.0 Run [ C] 60 Run Time [min] 24 * prepare matrix standards always without DNA Size Standard (ROX) Analysis of the matrix samples - Run the GeneScan software - File New Project (open folder of current run) Add Sample Files - Select a matrix sample in the Sample File column - Sample Raw Data - Check the matrix samples regarding a flat baseline. As shown in the figure below, there should be at least five peaks with peak heights about (Y-axis) for each matrix sample (optimal range: ) 3400 Data Points (X) 6400 Fig. 1 Electropherogram with raw data of the matrix standard 6-FAM - Select analysis range with flat baseline and re-inject the matrix sample if necessary - Note down start and end value (data points) of the analysis range, e.g. start value 3400, end value Calculate the difference, e.g = 3000 data points Mentype Nonaplex I NONAIGA01v1en

12 12 Generation of a new matrix - File New Matrix Fig. 2 Matrix sample selection - Import matrix samples for all dyes (B, G, Y, R) - Enter a Start At value, e.g Enter the calculated difference under Points, e.g Click on OK to calculate the new matrix Fig. 3 New matrix DS-30 - Save the matrix in the matrix folder: File Save as, e.g. Matrix DS-30 Matrix check Check the new matrix with current samples. - File New Project (open folder of the respective run) Add Sample Files - Select sample(s) in the Sample File column - Sample Install New Matrix (open matrix folder and select new matrix) - Re-analyse your samples There should be no pull-up peaks between the dye panels (B, G, Y, R) with the new matrix. Mentype Nonaplex I NONAIGA01v1en

13 13 Sample preparation Component Volume Hi-Di Formamide 12.0 µl DNA Size Standard 550 (ROX) 0.5 µl prepare 12 µl of the mix (formamide + DNA size standard) for all samples add 1 µl PCR product (diluted if necessary) or allelic ladder - Denaturation for 3 min at 95 C - Cool down to 4 C - For analysis: load the samples on the tray Signal intensities Options to increase the signal intensity: - Reduce the volume of the DNA Size Standard 550 (ROX) to peak heights of about 500 relative fluorescent units (RFU) - Purify the PCR products before starting the analysis Setting up the GeneScan software - Create a Sample Sheet and enter sample designation Injection list Component Set up Module File GS STR POP-4 (1 ml) D Matrix File e.g. Matrix DS-30 Size Standard e.g. SST_ROX_50-400bp Injection [s]* 5 Injection [kv] 15.0 Run [kv] 15.0 Run [ C] 60 Run Time [min]** 26 * Deviating from standard settings, the injection time may range between 1 and 10 s depending on the type of sample. If samples with very high signal intensities are recorded, a shorter injection time may be selected. For samples with low DNA content an injection time up to 10 s may be necessary. ** Depending on the analysis conditions the run time for Mentype Nonaplex I was modified in order to analyse fragments with lengths of up to 400 bp. Mentype Nonaplex I NONAIGA01v1en

14 14 Analysis parameter The recommended analysis parameters are: Analysis Range Start: 2000 Stop: Data Processing Baseline: Checked Multicomponent: Checked Smooth Options: Light Peak Detection Peak Amplitude Thresholds B:* Y:* G:* R:* Min. Peak Half Width: 2 pts Polynorminal Degree: 3 Peak Window Size: 11 pts** Size Call Range Min: 50 Max: 550 Size Calling Method Local Southern Method Split Peak Correction None * The peak amplitude threshold (cutoff value) corresponds to the minimum peak height that will be detected by the GeneScan or GeneMapper ID software. Thresholds are usually RFU and should be determined individually by the laboratory. Recommendation: The minimal peak height should be three times as high as the background noise of the baseline. ** Point alleles (i.e. alleles with at least 1 bp difference to the next integer allele) may occasionally not be distinguished. For improved peak detection, minimise the Peak Window Size further. Mentype Nonaplex I NONAIGA01v1en

15 Electrophoresis using the ABI PRISM 3130/3130xl Genetic Analyzer For detailed instructions on instrument setup, spectral calibration, or application of the ABI PRISM Data Collection software version 3.0 and the GeneMapper ID software, refer to the ABI PRISM 3130/3130xl Genetic Analyzers Getting Started Guide. The system with 4 capillaries is named ABI 3130 (former ABI 3100-Avant), and the system with 16 capillaries is named ABI 3130xl (former ABI 3100). The virtual filter set D shall be used for combined application of the four fluorescent labels 6-FAM, HEX, NED, and ROX (also called DS-30). Material Capillary 36 cm Capillary Array for 3130/3130xl Polymer POP-4 Polymer for 3130 Buffer 10x Genetic Analyzer Buffer with EDTA Spectral calibration / matrix generation Prior to conducting DNA fragment size analysis, it is necessary to perform a spectral calibration with the four fluorescent labels 6-FAM, HEX, NED, and ROX for each analyzer. The calibration procedure creates a matrix which is used to correct the overlapping of fluorescence emission spectra of the dyes. Spectral calibration comprises the following steps: - Preparation the spectral calibration standards - Loading the standards to the 96-well reaction plate (one sample per capillary) - Creating the instrument protocol for spectral calibration (Protocol Manager) - Defining the plate composition in the plate editor (Plate Manager) - Performing a spectral calibration run and checking the matrix Mentype Nonaplex I NONAIGA01v1en

16 16 Setting up the spectral calibration standards Example for 4 capillaries/abi 3130 Component Volume Hi-Di Formamide 47.5 µl Matrix standard DS µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-D1 - Denaturation for 3 min at 95 C - Cool down to 4 C Example for 16 capillaries/abi 3130xl Component Volume Hi-Di Formamide µl Matrix standard DS µl - Load 12 μl of the mix to a 96-well reaction plate, e.g. position A1-H1 and A2-H2 - Denaturation for 3 min at 95 C - Cool down to 4 C Performing spectral calibration run - Place the 96-well plate on the autosampler tray - In the Protocol Manager of the Data Collection software click New the window Instrument Protocol to open the Protocol Editor dialog box Instrument Protocol for spectral calibration Protocol Editor Name Type Dye Set Polymer* Array Length* Chemistry Run Module* Set up User (e.g. Spectral36_POP4_DS30) SPECTRAL D User (e.g. POP4) User (e.g. 36cm) Matrix Standard Default (e.g. Spect36_POP4_1) * Depends on the type of polymer and length of capillary used - Select OK to complete the Protocol Editor dialog box - In the Plate Manager of the Data Collection software click New to open the New Plate Dialog box Plate Editor for spectral calibration (I) New Plate Dialog Name Application Plate Type Owner Name / Operator Name Set up e.g. Spectral_DS-30_date Spectral Calibration 96-Well - Click on OK. A new table in the Plate Editor opens automatically Mentype Nonaplex I NONAIGA01v1en

17 17 Plate Editor for spectral calibration (II) Parameter Set up Sample Name Type name for the matrix samples Priority e.g. 100 Instrument Protocol 1 Spectral36_POP4_DS30 (setting described before) - Click into the column header to select the entire column, select Edit Fill Down to apply the information to all selected samples, and click on OK - In the Run Scheduler click on Find All, select Link to link the reaction plate on the autosampler up with the newly created plate record (position A or B) and start the run R, Y, G, B Fig. 4 Electropherogram of spectral calibration with matrix standard DS-30 on an ABI 3130 Matrix check - The quality value (Q value) of each capillary must be greater than 0.95 and the condition number range (C value) must be between 1 and Check the matrix samples for a flat baseline. As shown in the figure above, there should be four peaks with peak heights of about (Y-axis) in each matrix sample (optimal range: ) - Check the new matrix with your current samples. There should be no pull-up peaks between the dye panels (B, G, Y, R) with the new matrix - If calibration was not successful, use the optimised values and repeat the calibration run - If all capillaries have passed the test, the last calibration file for the Dye Set D is activated automatically in the Spectral Viewer. Rename the calibration file (e.g. DS-30_Date of calibration) using the respective button Mentype Nonaplex I NONAIGA01v1en

18 18 Sample preparation Component Volume Hi-Di Formamide 12.0 µl DNA Size Standard 550 (ROX) 0.5 µl prepare 12 µl of the mix (formamide + DNA size standard) for all samples add 1 µl PCR product (diluted if necessary) or allelic ladder - Denaturation for 3 min at 95 C - Cool down to 4 C - For analysis: load the samples on the tray Since injections take place simultaneously on all capillaries, 4 or 16 samples must be pipetted on the plate of multi-capillary analysers. If fewer samples are analysed, the empty positions must be filled with 12 µl Hi-Di Formamide. To ensure a reliable allelic assignment on multi-capillary analysers, several ladders should be run. Room temperature may influence the performance of PCR products on multi-capillary instruments, so that shoulder peaks or split peaks occur especially at low temperatures. Pay attention to keeping ambient conditions as recommended by the instrument manufacturer. Signal intensities Options to increase the signal intensity: - Reduce the volume of the DNA Size Standard 550 (ROX) to peak heights of about 500 relative fluorescent units (RFU) - Purify the PCR products before starting the analysis Mentype Nonaplex I NONAIGA01v1en

19 19 Setting up the GeneMapper ID software Edit the Run Module as follows for the first run: - In the Module Manager of the Data Collection software click on New to open the Run Module Editor dialog box Run Module 3kV_10s_450bp Run Modul Editor Set up Oven Temperature [ C] Default Poly Fill Volume Default Current Stability [µa] Default PreRun Voltage [kv] Default PreRun Time [s] Default Injection Voltage [kv] 3.0 Injection Time [s]* 10 Voltage Number of Steps Default Voltage Step Interval Default Data Delay Time [s] Default Run Voltage [kv] Default Run Time [s]** 1320 * Deviating from the standard settings, the injection time may range between 1 and 20 s depending on the type of sample. If samples with very high signal intensities are recorded, a shorter injection time may be selected. For samples with low DNA content an injection time of up to 20 s may be necessary. ** Depending on the analysis conditions the run time for Mentype Nonaplex I was modified in order to be able to analyse fragments with lengths of up to 400 bp. - Click on Save As, enter the name of the new module (e.g. 3kV_10s_450bp) and confirm with OK - Click on Close to exit the Run Module Editor Starting the run - Place the prepared 96-well plate on the autosampler tray - In the Protocol Manager of the Data Collection software, click on New in the Instrument Protocol window to open the Protocol Editor dialog box Instrument Protocol Protocol Editor Name Type Run Module* Dye Set * parameter see above Set up e.g. Run36_POP4_DS-30_22min REGULAR 3kV_10s_450bp D - Click on OK to exit the Protocol Editor Mentype Nonaplex I NONAIGA01v1en

20 20 Prior to each run, it is necessary to create a plate definition as follows: - In the Plate Manager of the Data Collection software click on New to open the New Plate Dialog box GeneMapper Plate Editor (I) New Plate Dialog Set up Name e.g. Plate_DS-30_Date Application select GeneMapper Application Plate Type 96-Well Owner Name / Operator Name - Click OK. A new table in the Pate Editor opens automatically GeneMapper Plate Editor (II) Parameter Set up Sample Name Type name for the samples Priority e.g. 100 (Default) Sample Type Sample or Allelic Ladder Size Standard e.g. SST-ROX_50-400bp Panel e.g. Biotype_Panels_v3a (choose test kit) Analysis Method e.g. Analysis_HID_3130 Snp Set - User-defined Results Group 1 (select results group) Instrument Protocol 1 Run36_POP4_DS-30 (setting described earlier) - Click into the column header to select the entire column, select Edit Fill Down to apply the information to all selected samples and click on OK - In the Run Scheduler, click on Find All, select Link to link the reaction plate on the autosampler up with the newly created plate record (position A or B) and start the run - During the run, view Error Status in the Event Log or examine the quality of the raw data for each capillary in the Capillaries Viewer or the Cap/Array Viewer - View data as overview in Run History or Cap/Array Viewer of the Data Collection software. Run data are saved in the Run Folder of the previously chosen Result Group. Mentype Nonaplex I NONAIGA01v1en

21 21 Analysis parameter / analysis method The recommended settings in the worksheet Peak Detector are: Peak Detection Algorithm Ranges Smoothing and Baselining Size Calling Method Peak Detection Advanced Analysis: Partial Range Start Pt: 2000; Stop Pt: Sizing: All Sizes Smoothing: Light Baseline Window: 51 pts Local Southern Method Peak Amplitude Thresholds B:* Y:* G:* R:* Min. Peak Half Width: 2 pts Polynominal Degree: 3 Peak Window Size: 11 pts** Slope Thresholds: 0.0 * The peak amplitude threshold (cutoff value) corresponds to the minimum peak height that will be detected by the GeneMapper ID software. The thresholds are usually RFU and should be determined individually by the laboratory. Recommendation: The minimal peak height should be three times as high as the background noise of the baseline. ** Point alleles (i.e. alleles with at least 1 bp difference to the next integer allele) may occasionally not be distinguished. For improved peak detection, minimise the Peak Window Size further. Mentype Nonaplex I NONAIGA01v1en

22 22 3. Analysis For general instructions on automatic sample analysing, refer to the GeneScan or GeneMapper ID Software User s Manual. Finding the exact lengths of the amplified products depends on the device type, the conditions of electrophoresis, as well as the DNA size standard used. Due to the complexity of some loci, determining the size should be based on evenly distributed references. The DNA Size Standard 550 (ROX) shall thus be used with the following lengths of fragments: 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 190, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400, 425, 450, 475, 500, 525, and 550 bp. Fig. 5 Electropherogram of the DNA Size Standard 550 (ROX), fragments with lengths in bp Note: The basic template files for the DNA Size Standard 550 (ROX) has to be adjusted to 400 bp within the GeneMapper ID software. The new template could be saved as e.g. SST-ROX_50-400bp and used for further analyses. Mentype Nonaplex I NONAIGA01v1en

23 23 4. Biotype template files Allele allocation should be carried out with a suitable analysis software, e.g. GeneMapper ID or Genotyper software in combination with the Mentype Nonaplex I template files from Biotype. Template files are available from our homepage or as CD-ROM on request. Recommended Biotype templates for GeneMapper ID/ID-X software are: Panels Biotype_Panels_v3a/v3X (choose kit) or higher versions BinSets Biotype_Bins_v3a/v3X or higher versions Size Standard SST-BTO_50-500bp (adjust up to 400bp, adjustment described earlier) Analysis Method Analysis_HID_310 Analysis_HID_3130 Analysis_HID_310_50rfu Analysis_HID_3130_50rfu Plot Settings Plots_4dyes Table Settings Table for 2 alleles Table for 10 alleles Panels and BinSets always have to be used whereas the other template files are optional. Additional Biotype templates for GeneMapper ID-X Software: Stutter* Biotype_Stutter_v3X or higher version * When loading the above mentioned panels, the stutter settings will not be accepted. Thus, the stutter data has to be imported separately. Recommended Biotype template files for Genotyper software are: Nonaplex I_v3e or higher versions General procedure for the analysis 1. Check the DNA size standard 2. Check the allelic ladder 3. Check the positive control 4. Check the negative control 5. Analyse and interpret the sample data Mentype Nonaplex I NONAIGA01v1en

24 24 5. Controls The Control DNA XY1 of the test kit and other commercially available DNA from standard cell lines represent the following alleles: Table 3. Allele assignment of Mentype Nonaplex I Locus Control ATCC CCR CCR CCR DNA XY1 K A Amelogenin X / Y X / X X / X X / Y X / Y D3S / / / / / 18 D8S / / / / / 16 D18S51 12 / / / / / 20 D21S11 27 / / 30 / / / / 29 FGA 20 / / / / / 23 SE33 17 / / / / / 27.2 THO1 6 / / / / / 9.3 vwa 15 / / / / / 19 For further confirmation, the table above displays the alleles of the reference DNA purchased from ATCC ( as well as three reference DNA purchased from Coriell Cell Repositories (CCR; that is up to standard of Szibor et al. (2003). 6. Lengths of fragments and alleles Table 4 to Table 6 show the fragment lengths of individual alleles that refer to the DNA Size Standard 550 (ROX). All analyses have been performed on an ABI PRISM 310/3130 Genetic Analyzer with POP-4 polymer. Different analysis instruments, DNA size standards or polymers may result in different fragment lengths. In addition, a visual alignment with the allelic ladder is recommended. Scaling Horizontal: bp Vertical: Depending on signal intensity Mentype Nonaplex I NONAIGA01v1en

25 25 Figure 6 AM D3S1358 THO1 SE33 vwa FGA D18S51 D8S1179 D21S11 (ROX) DNA Size Standard 550 Fig. 6 Electropherogram of the Mentype Nonaplex I using 500 pg Control DNA XY1. Analysis was performed on an ABI PRISM 310 Genetic Analyzer with the DNA Size Standard 550 (ROX). Allele assignment was performed using the Genotyper software and the Mentype Nonaplex I template file. Mentype Nonaplex NONAGIA01v1en

26 26 Figure 7 Fig. 7 Electropherogram of the allelic ladder Mentype Nonaplex I analysed on an ABI PRISM 310 Genetic Analyzer. Allele assignment was performed using the Genotyper software and the Mentype Nonaplex I template files. Mentype Nonaplex I NONAIGA01v1en

27 27 Table 4. Fragment lengths of the allelic ladder Mentype Nonaplex I analysed on an ABI PRISM 310 Genetic Analyzer (blue panel) Marker/allele Size [bp]* Further alleles** Marker/allele Size [bp]* Further alleles** Marker/allele Size [bp]* Amelogenin 6-FAM SE33 6-FAM SE33 6-FAM X , Y Further alleles** D3S FAM , , , , , TH01 6-FAM ,39, For a better orientation, these alleles are heightened within the allelic ladder Mentype Nonaplex NONAGIA01v1en

28 28 Table 5. Fragment lengths of the allelic ladder Mentype Nonaplex I analysed on an ABI PRISM 310 Genetic Analyzer (green panel) Marker/allel e Size [bp]* Further alleles** Marker/allel e Size [bp]* Further alleles** Marker/allel e Size [bp]* vwa HEX FGA HEX D18S51 HEX , 15, 16.1 Further alleles** , , , 23, , , 29 Mentype Nonaplex I NONAIGA01v1en

29 29 Table 6. Fragment lengths of the allelic ladder Mentype Nonaplex I analysed on an ABI PRISM 310 Genetic Analyzer (yellow panel) Marker/allele Size [bp]* Further alleles** Marker/allele Size [bp]* Further alleles** D8S1179 NED D21S11 NED , 24, 24.2, , , , 36, , 38, 38.2, 39 * rounded to integer ** The off-ladder alleles of Biotype s DNA pool are allocated with the actual Biotype template files for GeneMapper ID or Genotyper software. For further alleles see amongst others Mentype Nonaplex NONAGIA01v1en

30 30 7. Interpretation of results As mentioned above, post PCR analysis and automatic allele assignment with suitable analysis software ensure a precise and reliable discrimination of alleles. Pull-up peaks Pull-up peaks may occur if peak heights are outside the linear detection range (>3000 RFU), or if an incorrect matrix was applied. They appear at positions of specific peaks in other colour channels, typically with lower signal intensities. Peak heights should not exceed 3000 RFU in order to prevent pull-up peaks. Stutter peaks The occurrence of stutter peaks depends on the sequence of the repeat structure and the number of alleles. n-4 peaks are caused by a loss of a repeat unit during amplification of tetranucleotide STR motives, caused by slippage effects of the Taq DNA Polymerase. Interpretation of those peaks should be done in accordance with the Template Files of the Genotyper and GeneMapper ID software. Template-independent addition of nucleotides Because of its terminal transferase activity, the Taq DNA Polymerase tends to add an adenosine radical at the 3 -end of the amplified DNA fragments. The artefact peak is one base shorter than expected (-1 peaks). All Biotype primers are designed to minimise these artefacts. Artefact formation is further reduced by the final extension step of the PCR protocol at 68 C for 60 minutes. Peak height of the artefact correlates with the amount of DNA. Laboratories should define their own limits for analysis of the peaks. Artefacts Room temperature may influence the performance of PCR products on multicapillary instruments, so that shoulder peaks or split peaks occur. If shoulder or split peaks appear, we recommend injecting the sample again. Mentype Nonaplex NONAIGA01v1en

31 31 8. References Bär W, Brinkmann B, Budowle B, Carracedo A, Gill P, Lincoln P, Mayr W, Olaisen B (1997) DNA recommendations. Further report of the DNA Commission of the ISFG regarding the use of short tandem repeat systems. Int. J. Legal Med. 110: Szibor R, Edelmann J, Hering S, Plate I, Wittig H, Roewer L, Wiegand P, Calì F, Romano V, Michael M (2003) Cell line DNA typing in forensic genetics the necessity of reliable standards. Forensic Sci. Int Mentype Nonaplex NONAGA01v1en